Glycobioinformatics: current strategies and tools for data mining in MS-based glycoproteomics.

Glycobioinformatics is a rapidly developing field providing a vital support for MS-based glycoproteomics research. Recent advances in MS greatly increased technological capabilities for high throughput glycopeptide analysis. However, interpreting MS output, in terms of identifying glycan structures, attachment sites and glycosylation linkages still presents multiple challenges. Here, we discuss current strategies used in MS-based glycoproteomics and bioinformatics tools available for MS-based glycopeptide and glycan analysis. We also provide a brief overview of recent efforts in glycobioinformatics such as the new initiative UniCarbKB directed toward developing more comprehensive and unified glycobioinformatics platforms. With regards to glycobioinformatics tools and applications, we do not express our personal preferences or biases, but rather focus on providing a concise description of main features and functionalities of each application with the goal of assisting readers in making their own choices and identifying and locating glycobioinformatics tools most suitable for achieving their experimental objectives.

Corneal injury is associated with stromal and vascular alterations within cranial dura mater.

The cornea and cranial dura mater share sensory innervation. This link raises the possibility that pathological impulses mediated by corneal injury may be transmitted to the cranial dura, trigger dural perivascular/connective tissue nociceptor responses, and induce vascular and stromal alterations affecting dura mater blood and lymphatic vessel functionality. In this study, using a mouse model, we demonstrate for the first time that two weeks after the initial insult, alkaline injury to the cornea leads to remote pathological changes within the coronal suture area of the dura mater. Specifically, we detected significant pro-fibrotic changes in the dural stroma, as well as vascular remodeling characterized by alterations in vascular smooth muscle cell (VSMC) morphology, reduced blood vessel VSMC coverage, endothelial cell expression of the fibroblast specific protein 1, and significant increase in the number of podoplanin-positive lymphatic sprouts. Intriguingly, the deficiency of a major extracellular matrix component, small leucine-rich proteoglycan decorin, modifies both the direction and the extent of these changes. As the dura mater is the most important route for the brain metabolic clearance, these results are of clinical relevance and provide a much-needed link explaining the association between ophthalmic conditions and the development of neurodegenerative diseases.

Changes in dynamics of tumor/endothelial cell adhesive interactions depending on endothelial cell growth state and elastic properties.

Cancer cell adhesion to the endothelium is a crucial process in hematogenous metastasis, but how the integrity of the endothelial barrier and endothelial cell (EC) mechanical properties influence the adhesion between metastatic cancer cells and the endothelium remain unclear. In the present study, we have measured the adhesion between single cancer cells and two types of ECs at various growth states and their mechanical properties (elasticity) using atomic force microscopy single cell force spectroscopy. We demonstrated that the EC stiffness increased and adhesion with cancer cells decreased, as ECs grew from a single cell to a confluent state and developed cell-cell contacts, but this was reversed when confluent cells returned to a single state in a scratch assay. Our results suggest that the integrity of the endothelial barrier is an important factor in reducing the ability of the metastatic tumor cells to adhere to the vascular endothelium, extravasate and lodge in the vasculature of a distant organ where secondary metastatic tumors would develop.

Multi-focus Image Fusion for Confocal Microscopy Using U-Net Regression Map.

Characterizing the spatial relationship between blood vessel and lymphatic vascular structures, in the mice dura mater tissue, is useful for modeling fluid flows and changes in dynamics in various disease processes. We propose a new deep learning-based approach to fuse a set of multi-channel single-focus microscopy images within each volumetric z-stack into a single fused image that accurately captures as much of the vascular structures as possible. The red spectral channel captures small blood vessels and the green fluorescence channel images lymphatics structures in the intact dura mater attached to bone. The deep architecture Multi-Channel Fusion U-Net (MCFU-Net) combines multi-slice regression likelihood maps of thin linear structures using max pooling for each channel independently to estimate a slice-based focus selection map. We compare MCFU-Net with a widely used derivative-based multi-scale Hessian fusion method [8]. The multi-scale Hessian-based fusion produces dark-halos, non-homogeneous backgrounds and less detailed anatomical structures. Perception based no-reference image quality assessment metrics PIQUE, NIQE, and BRISQUE confirm the effectiveness of the proposed method.

Complex Non-sinus-associated Pachymeningeal Lymphatic Structures: Interrelationship With Blood Microvasculature.

The contribution of cranial dura mater vascular networks, as means for maintaining brain fluid movement and balance, and as the source of significant initiators and/or contributors to neurological disorders, has been overlooked. These networks consist of both blood and lymphatic vessels. The latter were discovered recently and described as sinus-associated structures thus changing the old paradigm that central nervous system lacks lymphatics. In this study, using markers specific to blood and lymphatic endothelia, we demonstrate the existence of the complex non-sinus-associated pachymeningeal lymphatic vasculature. We further show the interrelationship and possible connections between lymphatic vessels and the dural blood circulatory system. Our novel findings reveal the presence of lymphatic-like structures that exist on their own and/or in close proximity to microvessels. Of particular interest are sub-sets of vascular complexes with dual (lymphatic and blood) vessel identity representing a unique microenvironment within the cranial dura. The close association of the systemic blood circulation and meningeal lymphatics achieved in these complexes could facilitate fluid exchange between the two compartments and constitute an alternative route for CSF drainage.

Applications of Atomic Force Microscopy for Adhesion Force Measurements in Mechanotransduction.

Adhesive interactions between living cells or ligand-receptor interactions can be studied at the molecular level using atomic force microscopy (AFM). Adhesion force measurements are performed with functionalized AFM probes. In order to measure single ligand-receptor interactions, a cantilever with a pyramidal tip is functionalized with a bio-recognized ligand (e.g., extracellular matrix protein). The ligand-functionalized probe is then brought into contact with a cell in culture to investigate adhesion between the respective probe-bound ligand and endogenously expressed cell surface receptors (e.g., integrins or other adhesion receptor). For experiments designed to examine cell-cell adhesions, a single cell is attached to a tipless cantilever which is then brought into contact with other cultured cells. Force curves are recorded to determine the forces necessary to rupture discrete adhesions between the probe-bound ligand and receptor, or to determine total adhesion force at cell-cell contacts. Here, we describe the procedures for measuring adhesions between (a) fibronectin and α5ß1 integrin, and (b) breast cancer cells and bone marrow endothelial cells.

Patch-Based Semantic Segmentation for Detecting Arterioles and Venules in Epifluorescence Imagery.

Segmentation and quantification of microvasculature structures are the main steps toward studying microvasculature remodeling. The proposed patch based semantic architecture enables accurate segmentation for the challenging epifluorescence microscopy images. Our pixel-based fast semantic network trained on random patches from different epifluorescence images to learn how to discriminate between vessels versus nonvessels pixels. The proposed semantic vessel network (SVNet) relies on understanding the morphological structure of the thin vessels in the patches rather than considering the whole image as input to speed up the training process and to maintain the clarity of thin structures. Experimental results on our ovariectomized - ovary removed (OVX) - mice dura mater epifluorescence microscopy images shows promising results in both arteriole and venule part. We compared our results with different segmentation methods such as local, global thresholding, matched based filter approaches and related state of the art deep learning networks. Our overall accuracy (> 98%) outperforms all the methods including our previous work (VNet). [1].

Temporal and molecular dynamics of human metastatic breast carcinoma cell adhesive interactions with human bone marrow endothelium analyzed by single-cell force spectroscopy.

Bone is a common site of metastasis for breast cancer and the mechanisms of metastasis are not fully elucidated. The purpose of our study was to characterize temporal and molecular dynamics of adhesive interactions between human breast cancer cells (HBCC) and human bone marrow endothelium (HBME) with piconewton resolution using atomic force microscopy (AFM). In adhesion experiments, a single breast cancer cell, MDA-MB-231 (MB231) or MDA-MB-435 (MB435) was attached to the AFM cantilever and brought into contact with a confluent HBME monolayer for different time periods (0.5 to 300 sec). The forces required to rupture individual molecular interactions and completely separate interacting cells were analyzed as measures of cell-cell adhesion. Adhesive interactions between HBME and either MB231 or MB435 cells increased progressively as cell-cell contact time was prolonged from 0.5 to 300 sec due to the time-dependent increase in the number and frequency of individual adhesive events, as well as to the involvement of stronger ligand-receptor interactions over time. Studies of the individual molecule involvement revealed that Thomsen-Friedenreich antigen (TF-Ag), galectin-3, integrin-ß1, and integrin-α3 are all contributing to HBCC/HBME adhesion to various degrees in a temporally defined fashion. In conclusion, cell-cell contact time enhances adhesion of HBCC to HBME and the adhesion is mediated, in part, by TF-Ag, galectin-3, integrin-α3, and integrin-ß1.

Estrogen-Dependent Changes in Dura Mater Microvasculature Add New Insights to the Pathogenesis of Headache.

The pathogenesis of headaches is a matter of ongoing discussion of two major theories describing it either as a vascular phenomenon resulting from vasodilation or primarily as a neurogenic process accompanied by secondary vasodilation associated with sterile neurogenic inflammation. While summarizing current views on neurogenic and vascular origins of headache, this mini review adds new insights regarding how smooth muscle-free microvascular networks, discovered within dura mater connective tissue stroma (previously thought to be "avascular"), may become a site of initial insult generating the background for the development of headache. Deficiencies in estrogen-dependent control of microvascular integrity leading to plasma protein extravasation, potential activation of perivascular and connective tissue stroma nociceptive neurons, and triggering of inflammatory responses are described. Finally, possible avenues for controlling and preventing these pathophysiological changes are discussed.

Cell surface Thomsen-Friedenreich proteome profiling of metastatic prostate cancer cells reveals potential link with cancer stem cell-like phenotype.

The tumor-associated Thomsen-Friedenreich glycoantigen (TF-Ag) plays an important role in hematogenous metastasis of multiple cancers. The LTQ Orbitrap LC-MS/MS mass spectrometry analysis of cell surface TF-Ag proteome of metastatic prostate cancer cells reveals that several cell surface glycoproteins expressing this carbohydrate antigen in prostate cancer (CD44, α2 integrin, ß1 integrin, CD49f, CD133, CD59, EphA2, CD138, transferrin receptor, profilin) are either known as stem cell markers or control important cancer stem-like cell functions. This outcome points to a potential link between TF-Ag expression and prostate cancer stem-like phenotype. Indeed, selecting prostate cancer cells for TF-Ag expression resulted in the enrichment of cells with stem-like properties such as enhanced clonogenic survival and growth, prostasphere formation under non-differentiating and differentiating conditions, and elevated expression of stem cell markers such as CD44 and CD133. Further, the analysis of the recent literature demonstrates that TF-Ag is a common denominator for multiple prostate cancer stem-like cell populations identified to date and otherwise characterized by distinct molecular signatures. The current paradigm suggests that dissemination of tumor cells with stem-like properties to bone marrow that occurred before surgery and/or radiation therapy is largely responsible for disease recurrence years after radical treatment causing a massive clinical problem in prostate cancer. Thus, developing means for destroying disseminated prostate cancer stem-like cells is an important goal of modern cancer research. The results presented in this study suggest that multiple subpopulation of putative prostate cancer stem-like cells characterized by distinct molecular signatures can be attacked using a single target commonly expressed on these cells, the TF-Ag.

Humanization of JAA-F11, a Highly Specific Anti-Thomsen-Friedenreich Pancarcinoma Antibody and InVitro Efficacy Analysis.

JAA-F11 is a highly specific mouse monoclonal to the Thomsen-Friedenreich Antigen (TF-Ag) which is an alpha-O-linked disaccharide antigen on the surface of ~80% of human carcinomas, including breast, lung, colon, bladder, ovarian, and prostate cancers, and is cryptic on normal cells. JAA-F11 has potential, when humanized, for cancer immunotherapy for multiple cancer types. Humanization of JAA-F11, was performed utilizing complementarity determining regions grafting on a homology framework. The objective herein is to test the specificity, affinity and biology efficacy of the humanized JAA-F11 (hJAA-F11). Using a 609 target glycan array, 2 hJAA-F11 constructs were shown to have excellent chemical specificity, binding only to TF-Ag alpha-linked structures and not to TF-Ag beta-linked structures. The relative affinity of these hJAA-F11 constructs for TF-Ag was improved over the mouse antibody, while T20 scoring predicted low clinical immunogenicity. The hJAA-F11 constructs produced antibody-dependent cellular cytotoxicity in breast and lung tumor lines shown to express TF-Ag by flow cytometry. Internalization of hJAA-F11 into cancer cells was also shown using a surface binding ELISA and confirmed by immunofluorescence microscopy. Both the naked hJAA-F11 and a maytansine-conjugated antibody (hJAA-F11-DM1) suppressed in vivo tumor progression in a human breast cancer xenograft model in SCID mice. Together, our results support the conclusion that the humanized antibody to the TF-Ag has potential as an adjunct therapy, either directly or as part of an antibody drug conjugate, to treat breast cancer, including triple negative breast cancer which currently has no targeted therapy, as well as lung cancer.

Intravascular metastatic cancer cell homotypic aggregation at the sites of primary attachment to the endothelium.

The two major theories of cancer metastasis, the seed and soil hypothesis and the mechanical trapping theory, view tumor cell adhesion to blood vessel endothelia and cancer cell aggregation as corresponding key components of the metastatic process. Here, we demonstrate in vitro, ex vivo, and in vivo that metastatic breast and prostate carcinoma cells form multicellular homotypic aggregates at the sites of their primary attachment to the endothelium. Our results suggest that metastatic cell heterotypic adhesion to the microvascular endothelium and homotypic aggregation represent two coordinated subsequent steps of the metastatic cascade mediated largely by similar molecular mechanisms, specifically by interactions of tumor-associated Thomsen-Friedenreich glycoantigen with the beta-galactoside-binding protein, galectin-3. In addition to inhibiting neoplastic cell adhesion to the endothelium and homotypic aggregation, disrupting this line of intercellular communication using synthetic Thomsen-Friedenreich antigen masking and Thomsen-Friedenreich antigen mimicking compounds greatly affects cancer cell clonogenic survival and growth as well. Thus, beta-galactoside-mediated intravascular heterotypic and homotypic tumor cell adhesive interactions at the sites of a primary attachment to the microvascular endothelium could play an important role during early stages of hematogenous cancer metastasis.

Confocal Vessel Structure Segmentation with Optimized Feature Bank and Random Forests.

In this paper, we consider confocal microscopy based vessel segmentation with optimized features and random forest classification. By utilizing multi-scale vessel-specific features tuned to capture curvilinear structures such as Frobenius norm of the Hessian eigenvalues, Laplacian of Gaussians (LoG), oriented second derivative, line detector and intensity masked with LoG scale map. we obtain better segmentation results in challenging imaging conditions. We obtain binary segmentations using random forest classifier trained on physiologists marked ground-truth. Experimental results on mice dura mater confocal microscopy vessel segmentations indicate that we obtain better results compared to global segmentation approaches.

Random Forests for Dura Mater Microvasculature Segmentation Using Epifluorescence Images.

Automatic segmentation of microvascular structures is a critical step in quantitatively characterizing vessel remodeling and other physiological changes in the dura mater or other tissues. We developed a supervised random forest (RF) classifier for segmenting thin vessel structures using multiscale features based on Hessian, oriented second derivatives, Laplacian of Gaussian and line features. The latter multiscale line detector feature helps in detecting and connecting faint vessel structures that would otherwise be missed. Experimental results on epifluorescence imagery show that the RF approach produces foreground vessel regions that are almost 20 and 25 percent better than Niblack and Otsu threshold-based segmentations respectively.

Multiquadric Spline-Based Interactive Segmentation of Vascular Networks.

Commonly used drawing tools for interactive image segmentation and labeling include active contours or boundaries, scribbles, rectangles and other shapes. Thin vessel shapes in images of vascular networks are difficult to segment using automatic or interactive methods. This paper introduces the novel use of a sparse set of user-defined seed points (supervised labels) for precisely, quickly and robustly segmenting complex biomedical images. A multiquadric spline-based binary classifier is proposed as a unique approach for interactive segmentation using as features color values and the location of seed points. Epifluorescence imagery of the dura mater microvasculature are difficult to segment for quantitative applications due to challenging tissue preparation, imaging conditions, and thin, faint structures. Experimental results based on twenty epifluorescence images is used to illustrate the benefits of using a set of seed points to obtain fast and accurate interactive segmentation compared to four interactive and automatic segmentation approaches.

Mechanical entrapment is insufficient and intercellular adhesion is essential for metastatic cell arrest in distant organs.

In this report, we challenge a common perception that tumor embolism is a size-limited event of mechanical arrest, occurring in the first capillary bed encountered by blood-borne metastatic cells. We tested the hypothesis that mechanical entrapment alone, in the absence of tumor cell adhesion to blood vessel walls, is not sufficient for metastatic cell arrest in target organ microvasculature. The in vivo metastatic deposit formation assay was used to assess the number and location of fluorescently labeled tumor cells lodged in selected organs and tissues following intravenous inoculation. We report that a significant fraction of breast and prostate cancer cells escapes arrest in a lung capillary bed and lodges successfully in other organs and tissues. Monoclonal antibodies and carbohydrate-based compounds (anti-Thomsen-Friedenreich antigen antibody, anti-galectin-3 antibody, modified citrus pectin, and lactulosyl-l-leucine), targeting specifically beta-galactoside-mediated tumor-endothelial cell adhesive interactions, inhibited by >90% the in vivo formation of breast and prostate carcinoma metastatic deposits in mouse lung and bones. Our results indicate that metastatic cell arrest in target organ microvessels is not a consequence of mechanical trapping, but is supported predominantly by intercellular adhesive interactions mediated by cancer-associated Thomsen-Friedenreich glycoantigen and beta-galactoside-binding lectin galectin-3. Efficient blocking of beta-galactoside-mediated adhesion precludes malignant cell lodging in target organs.

Continuous real time ex vivo epifluorescent video microscopy for the study of metastatic cancer cell interactions with microvascular endothelium.

Recent studies suggest that only endothelium-attached malignant cells are capable of giving rise to hematogenous cancer metastases. Moreover, tumor cell adhesion to microvascular endothelium could be crucial in metastasis predilection to specific organs or tissues. However, the existing in vitro and in vivo techniques do not provide for sufficient delineation of distinct stages of a dynamic multi-step intravascular adhesion process. Here we report the development of an experimental system allowing for prolonged continuous ex vivo real-time observation of malignant cell adhesive interactions with perfused microvessels of a target organ in the context of its original tissue. Specifically, the vasculature of excised dura mater perfused with prostate cancer cells is described. An advantage of this technique is that selected fluorescently labeled tumor cells can be followed along identified vascular trees across the entire tissue specimen. The techniques provide for superior microvessel visualization and allow for uninterrupted monitoring and video recording of subsequent adhesion events such as rolling, docking (initial reversible adhesion), locking (irreversible adhesion), and flattening of metastatic cancer cells within perfused microvasculature on a single cell level. The results of our experiments demonstrate that intravascular adhesion of cancer cells differs dramatically from such of the leukocytes. Within dura microvessels perfused at physiological rate, non-interacting, floating, tumor cells move at velocities averaging 7.2 x 10(3) microm/s. Some tumor cells, similarly to leukocytes, exhibit rolling-like motion patterns prior to engaging into more stable adhesive interactions. In contrast, other neoplastic cells became stably adhered without rolling showing a rapid reduction in velocity from 2 x 10(3) to 0 microm/s within fractions of a second. The experimental system described herein, while developed originally for studying prostate cancer cell interactions with porcine dura mater microvasculature, offers great flexibility in adhesion experiments design and is easily adapted for use with a variety of other tissues including human.

Endothelial integrin α3ß1 stabilizes carbohydrate-mediated tumor/endothelial cell adhesion and induces macromolecular signaling complex formation at the endothelial cell membrane.

Blood borne metastatic tumor cell adhesion to endothelial cells constitutes a critical rate-limiting step in hematogenous cancer metastasis. Interactions between cancer associated carbohydrate Thomsen-Friedenreich antigen (TF-Ag) and endothelium-expressed galectin-3 (Gal-3) have been identified as the leading molecular mechanism initiating tumor/endothelial cell adhesion in several types of cancer. However, it is unknown how these rather weak and transient carbohydrate/lectin mediated interactions are stabilized. Here, using Western blot and LC tandem mass spectrometry analyses of pull-downs utilizing TF-Ag loaded gold nanoparticles, we identified Gal-3, endothelial integrin α3ß1, Src kinase, as well as 5 additional molecules mapping onto focal adhesion pathway as parts of the macromolecular complexes formed at the endothelial cell membranes downstream of TF-Ag/Gal-3 interactions. In a modified parallel flow chamber assay, inhibiting α3ß1 integrin greatly reduced the strength of tumor/endothelial cell interactions without affecting the initial cancer cell adhesion. Further, the macromolecular complex induced by TF-Ag/Gal-3/α3ß1 interactions activates Src kinase, p38, and ERK1/2, pathways in endothelial cells in a time- and α3ß1-dependent manner. We conclude that, following the initial metastatic cell attachment to endothelial cells mediated by TF-Ag/Gal-3 interactions, endothelial integrin α3ß1 stabilizes tumor/endothelial cell adhesion and induces the formation of macromolecular signaling complex activating several major signaling pathways in endothelial cells.

Multi-focus image fusion using epifluorescence microscopy for robust vascular segmentation.

Automatic segmentation of three-dimensional mi-crovascular structures is needed for quantifying morphological changes to blood vessels during development, disease and treatment processes. Single focus two-dimensional epifluorescent imagery lead to unsatisfactory segmentations due to multiple out of focus vessel regions that have blurred edge structures and lack of detail. Additional segmentation challenges include varying contrast levels due to diffusivity of the lectin stain, leakage out of vessels and fine morphological vessel structure. We propose an approach for vessel segmentation that combines multi-focus image fusion with robust adaptive filtering. The robust adaptive filtering scheme handles noise without destroying small structures, while multi-focus image fusion considerably improves segmentation quality by deblurring out-of-focus regions through incorporating 3D structure information from multiple focus steps. Experiments using epifluorescence images of mice dura mater show an average of 30.4% improvement compared to single focus microvasculature segmentation.

Pulsed estrogen therapy prevents post-OVX porcine dura mater microvascular network weakening via a PDGF-BB-dependent mechanism.

In postmenopausal women, estrogen (E2) deficiencies are frequently associated with higher risk of intracranial hemorrhage, increased incidence of stroke, cerebral aneurysm, and decline in cognitive abilities. In younger postpartum women and those using oral contraceptives, perturbations in E2 are associated with higher risk of cerebral venous thrombosis. A number of serious intracranial pathologic conditions linked to E2 deficiencies, such as dural sinus thrombosis, dural fistulae, non-parenchymal intracranial hemorrhages, migraines, and spontaneous cerebrospinal fluid leaks, involve the vessels not of the brain itself, but of the outer fibrous membrane of the brain, the dura mater (DM). The pathogenesis of these disorders remains mysterious and how estrogen regulates structural and functional integrity of DM vasculature is largely unknown. Here, we demonstrate that post ovariectomy (OVX) DM vascular remodeling is manifested by microvessel destabilization, capillary rarefaction, increased vascular permeability, and aberrant angio-architecture, and is the result of disrupted E2-regulated PDGF-BB signaling within dura microvasculature. These changes, associated with the reduction in systemic PDGF-BB levels, are not corrected by a flat-dose E2 hormone replacement therapy (HRT), but are largely prevented using HRT schedules mimicking physiological E2 fluctuations. We demonstrate that 1) E2 regulates PDGF-BB production by endothelial cells in a dose-dependent manner and 2) optimization of PDGF-BB levels and induction of robust PDGF-mediated endothelial cell-vascular pericyte interactions require high (estrous) E2 concentrations. We conclude that high (estrous) levels of E2 are important in controlling PDGF-mediated crosstalk between endothelial cells and pericytes, a fundamental mechanism governing microvessel stability and essential for preserving intracranial homeostasis.